I ran camera() in edgeR to test whether 2 gene sets are highly ranked in my mutant data compared to my wild-type data in terms of differential expression relative to other genes.
design <- model.matrix(~0 + genotype)
contrast <- makeContrasts(mutant - wildtype, levels=design)
camera_test <- camera(y, id_matrix, design=design, contrast = contrast)
|wildtype vs mutant||NGenes||Direction||PValue||FDR|
|Gene set 1||1879||Down||1.92E-20||4.2E-20|
|Gene set 2||4196||Down||2.76E-13||3.1E-13|
To follow up on these results, I would like to test whether the difference in rank between these 2 gene sets is significant, i.e. to test whether Gene set 1 is more significantly downregulated in the mutant than Gene set 2. What is the best way to approach this? Thank you.